Exploiting long-range dependencies in protein β-sheet secondary structure prediction

Authors:
Yizhao Ni;Mahesan Niranjan
Affiliations:
ISIS Group, School of Electronics and Computer Science, University of Southampton, UK;ISIS Group, School of Electronics and Computer Science, University of Southampton, UK
Venue:
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
Year:
2010

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Abstract

We investigate if interactions of longer range than typically considered in local protein secondary structure prediction methods can be captured in a simple machine learning framework to improve the prediction of β sheets. We use support vector machines and recursive feature elimination to show that the small signals available in long range interactions can indeed be exploited. The improvement is small but statistically significant on the benchmark datasets we used. We also show that feature selection within a long window and over amino acids at specific positions typically selects amino acids that are shown to be more relevant in the initiation and termination of β-sheet formation.